Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017556.1 Corchorus olitorius cultivar O-4 contig17589, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5292
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:1325 original size:517 final size:516
Alignment explanation
Indices: 326--1304 Score: 1626
Period size: 517 Copynumber: 1.9 Consensus size: 516
316 CTGAGTATTG
* *
326 TGGCCAAAATTTGAGGAAAAATTTTTCGGATCTTTTTTTGCAAACTTTTAGCCGAAATCATGTAT
1 TGGCCAAAATTTGAGGAAAAATTTTTCGGATCTGTTTTTGCAAAATTTTAGCCGAAATCATGTAT
**
391 TATCCATCACAGTTTTGGGCTAAAAACGCGTTTGAGGCCCCTGGCTCAATTTTGCTTGATTTTTG
66 TATCCATCACAGTTTTAAGCTAAAAACGCGTTTGAGGCCCCTGGCTCAATTTTGCTTGATTTTTG
456 GCGCCTAGAAACCTTGAAATTTCAATATTCATCTAACCAAATCTCAACCACATTGAATTTAAAAT
131 GCGCCTAGAAACCTTGAAATTTCAATATTCATCTAACCAAATCTCAACCACATTGAATTTAAAAT
*
521 TTTGATTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGCAAAAAATTGG
196 TTTGATTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATTGG
* *
586 AAAAACGATATTAGAAGCGTGAAAAAGCCTTCAATATTTTTGGCGTTGATTTTTATATTTTTCTG
261 AAAAACGATATTAGAAGCGTGAAAAACCCTTCAATATTGTTGGCGTTGATTTTTATATTTTTCTG
651 AGTACTGTGGCCAAAATTTGAGGAAAAAATATTTCGGATCATTTTTTGCAAAATTTTAGCCGAAA
326 AGTACTGTGGCCAAAATTTGAGGAAAAAATATTTCGGATCATTTTTTGCAAAATTTTAGCCGAAA
* * * *
716 TCGTGTACTATCCATCACGGTTTTGGGCTAAAAACGCGTTCCCGGGTCCCGACACAGTTTTGCAT
391 TCGTGTACTATCCATCACGGTTTTGGGCTAAAAACACGTTCCAGGGCCCCGACACAATTTTGCAT
* * * *
781 GATTTTTTGGGAAAAGGCTCTTTGAAATATCTATATTGATCTTACCAAATTGGAAAAATTT
456 GATTTTTTGGGAAAAGACTCATTGAAATATCAATATTCATCTTACCAAATTGGAAAAATTT
842 TGGCC-AAATATTGAGGAAAAATTTTTCGGAT-TAGTTTTTGCAAAATTTGT-GCCGAAATCATG
1 TGGCCAAAAT-TTGAGGAAAAATTTTTCGGATCT-GTTTTTGCAAAATTT-TAGCCGAAATCATG
* * *
904 TATTATCCATCACGGTTTTAAGCTAAAAACGGGTTTTAGGCCCCTGGCTCAATTTTGCTTGATTT
63 TATTATCCATCACAGTTTTAAGCTAAAAACGCGTTTGAGGCCCCTGGCTCAATTTTGCTTGATTT
* *
969 TTGGCGCCTAGAACCCTTGGAAATTTCAATATTCATCTTACCAAATCTCAACCACATTGAATTTA
128 TTGGCGCCTAGAAACCTT-GAAATTTCAATATTCATCTAACCAAATCTCAACCACATTGAATTTA
*
1034 AAATTTTGATTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCTGAAAAAAA
192 AAATTTTGATTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAA
1099 TTGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATATTGTTGGCGTTGATTTTTATATTTT
257 TTGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATATTGTTGGCGTTGATTTTTATA-TTT
* * *
1164 TTCTGAGTATTGTTGCCAAAATTTGAGG-AAAAATATTTCGGTTCATTTTTTGCAAAATTTTAGC
321 TTCTGAGTACTGTGGCCAAAATTTGAGGAAAAAATATTTCGGATCATTTTTTGCAAAATTTTAGC
* * *
1228 CGAAATCGTGTACTATCCATCACGGTTTTTGGCTAAAAACACGTTCCAGGGCCCCGGCTCAATTT
386 CGAAATCGTGTACTATCCATCACGGTTTTGGGCTAAAAACACGTTCCAGGGCCCCGACACAATTT
1293 TGCAAT-ATTTTT
451 TGC-ATGATTTTT
1305 GGCGCCCCGA
Statistics
Matches: 434, Mismatches: 23, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
515 5 0.01
516 128 0.29
517 270 0.62
518 31 0.07
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (516 bp):
TGGCCAAAATTTGAGGAAAAATTTTTCGGATCTGTTTTTGCAAAATTTTAGCCGAAATCATGTAT
TATCCATCACAGTTTTAAGCTAAAAACGCGTTTGAGGCCCCTGGCTCAATTTTGCTTGATTTTTG
GCGCCTAGAAACCTTGAAATTTCAATATTCATCTAACCAAATCTCAACCACATTGAATTTAAAAT
TTTGATTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATTGG
AAAAACGATATTAGAAGCGTGAAAAACCCTTCAATATTGTTGGCGTTGATTTTTATATTTTTCTG
AGTACTGTGGCCAAAATTTGAGGAAAAAATATTTCGGATCATTTTTTGCAAAATTTTAGCCGAAA
TCGTGTACTATCCATCACGGTTTTGGGCTAAAAACACGTTCCAGGGCCCCGACACAATTTTGCAT
GATTTTTTGGGAAAAGACTCATTGAAATATCAATATTCATCTTACCAAATTGGAAAAATTT
Found at i:1701 original size:327 final size:326
Alignment explanation
Indices: 842--1852 Score: 1316
Period size: 327 Copynumber: 3.1 Consensus size: 326
832 GGAAAAATTT
* *
842 TGGCCAAATATTGAGGAAAAATTTTTCGGATTAGTTTTTGCAAAATTTGT-GCCGAAATCATGTA
1 TGGCCAAAAATTGAGGAAAAATTTTTCGGATAAGTTTTTGCAAAATTT-TAGCCGAAATC--GT-
* * ** * * *
906 TTATCCATCACGGTTTTAAGCTAAAAACGGGTTT-TAGGCCCCTGGCTCAATTTTGCTTGATTTT
62 GTA--CATCACAGTTTTTGGCTAAAAACGCGTTTCAAGGCCCC-GGCTCAATTTTGCATGATTTT
* *
970 TGGCGCCTAGAACCCTTGGAAATTTCAATATTCATCTTACCAAATCTCAACCACATTGAATTTAA
124 TGGCGCCTAGAACCCTT-GAAATTTCAATATTCATCTAACCAAATCTCAGCCACATTGAATTTAA
* * *
1035 AATTTTGATTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCTGAAAAAAAT
188 AAATTTGATTTTAAGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCCGAAAAAAA-
* * * * *
1100 TGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATATTGTTGGCGTTGATTTTTATATTTTT
252 TGGAAAAACGATATTAGAAGCGTG-AAAAGCCTTCAATATTCTTGGAGTTGAATTATATATTTTT
1165 TCTGAGTATTG
316 TCTGAGTATTG
* * * * * *
1176 TTGCCAAAATTTGAGGAAAAATATTTCGGTTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTAC
1 TGGCCAAAAATTGAGGAAAAATTTTTCGGATAAGTTTTTGCAAAATTTTAGCCGAAATCGTGTAC
* * *
1241 TATCCATCACGGTTTTTGGCTAAAAACACGTTCCAGGGCCCCGGCTCAATTTTGCAAT-ATTTTT
66 -AT-CA-CA--GTTTTTGGCTAAAAACGCGTTTCAAGGCCCCGGCTCAATTTTGC-ATGATTTTT
** * *
1305 GGCGCCCCGAACCATTGAAATTTCAATATTCATCTAACTAAATCTCAGCCACATTGAATTTAAAA
125 GGCGCCTAGAACCCTTGAAATTTCAATATTCATCTAACCAAATCTCAGCCACATTGAATTTAAAA
* *
1370 ATTTGATTTTAAGAGCATCTGAATATTATTTCGATTTAATTACG-AATTAATTCCGAAAAAAATG
190 ATTTGATTTTAAGAGCATCTGAATCTTGTTTCGATTTAATTA-GAAATTAATTCCGAAAAAAATG
* * * * *
1434 GGAAAACGATATTAAAAGCGTTAAAAGCTCTTCAATATTTTTGGTGTTGAATTATATATTTTTTC
254 GAAAAACGATATTAGAAGCGTGAAAAGC-CTTCAATATTCTTGGAGTTGAATTATATATTTTTTC
1499 TGAGTATTG
318 TGAGTATTG
1508 TGGCCAAAAATTGAGGAAAAATTTTTCGGATAAGTTTTTGCAAAATTTTAGCCGAAATCGTGTAC
1 TGGCCAAAAATTGAGGAAAAATTTTTCGGATAAGTTTTTGCAAAATTTTAGCCGAAATCGTGTAC
* * * **
1573 ATCACAGTTTTTGGCTAAAATCGCATTTCAAGGCCCCGGCTTAATTTTGCATGAACTTTGGCGCC
66 ATCACAGTTTTTGGCTAAAAACGCGTTTCAAGGCCCCGGCTCAATTTTGCATGATTTTTGGCGCC
* * * *
1638 TAGAGCCCTTGAAATTACTATATTCATCTAACCAAATCTCAGCCACAGTGAATTTAAAAATTTGA
131 TAGAACCCTTGAAATTTCAATATTCATCTAACCAAATCTCAGCCACATTGAATTTAAAAATTTGA
* *
1703 TTTTAAGAGCATCTGAATCCTGTTTCGATTTAATTAGAAATTAATT-C-AAACAAATGGAAAAAC
196 TTTTAAGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCCGAAAAAAATGGAAAAAC
* * *
1766 GATATTAGAAGCGTGAAAAGCCTTCAATCTTCTTGGAGTAGAAATATATATTTTTTCTGAGTATT
261 GATATTAGAAGCGTGAAAAGCCTTCAATATTCTTGGAGTTGAATTATATATTTTTTCTGAGTATT
1831 G
326 G
*
1832 TGG-CAAATAATTGAGAAAAAA
1 TGGCCAAA-AATTGAGGAAAAA
1853 AAATTTTGGG
Statistics
Matches: 593, Mismatches: 71, Indels: 36
0.85 0.10 0.05
Matches are distributed among these distances:
323 4 0.01
324 55 0.09
325 33 0.06
326 4 0.01
327 146 0.25
329 3 0.01
330 4 0.01
331 11 0.02
332 124 0.21
333 102 0.17
334 100 0.17
335 7 0.01
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Consensus pattern (326 bp):
TGGCCAAAAATTGAGGAAAAATTTTTCGGATAAGTTTTTGCAAAATTTTAGCCGAAATCGTGTAC
ATCACAGTTTTTGGCTAAAAACGCGTTTCAAGGCCCCGGCTCAATTTTGCATGATTTTTGGCGCC
TAGAACCCTTGAAATTTCAATATTCATCTAACCAAATCTCAGCCACATTGAATTTAAAAATTTGA
TTTTAAGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCCGAAAAAAATGGAAAAAC
GATATTAGAAGCGTGAAAAGCCTTCAATATTCTTGGAGTTGAATTATATATTTTTTCTGAGTATT
G
Found at i:2856 original size:327 final size:323
Alignment explanation
Indices: 2005--2954 Score: 1118
Period size: 320 Copynumber: 2.9 Consensus size: 323
1995 GAAAAAATTT
* *
2005 TGGCCAAAATTTGAGG-AAAATTTTATCGGATCAGTTTTTGCAAAATTTTAGCCGAAATCATGTA
1 TGGCCAAAAATTGAGGAAAAATTTT-TCGGATCAATTTTTGCAAAATTTTAGCCGAAATCATGTA
* * * * * * *
2069 CGATAGATCACGGTTTTTGGCTAAAAACGCGTTCCAAGCCCCCGGCTCAGTTTTTCTTGATTTTT
65 C--T--ATCACAGTTTTTGGCTAAAAACGCGTTTCAAGGCCTCGGCTCAATTTTGCATGATTTTT
** * * * *
2134 TACAG-CTAGAACCCTTGAAATTTTGATATTCATCTAACTAAATGTCAACCACATTAAATTTAAA
126 GGC-GCCTAGAACCCTTGAAATTCT-ATATTCATCTAACCAAATCTCAACCACATTGAATTTAAA
* * *
2198 ATTTTGATTTTACGAGCATCTGAATCTTGTTTCTATTTAATTA-G-A--AATT----AATTGGGA
189 AATTTGATTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGGAATTAATTCAAAAAATGGGA
* * * *
2255 AAACGATATTGGAAGCGTGAAAAACCTTCAATACTTTTGGCGTTGATTTTTATATTTGTCCTAAG
254 AAACGATATTAGAAGCGTGAAAAGCCTTCAATACTTTTGGCGTTGAATTATATATTTGTCCTAAG
*
2320 TATTG
319 TATAG
* *
2325 TGGCCAAAAATTGAGGAAAAATTTTTCGGATCATTTTTTGCAAAATTTTAGCCGAAATCGTGTAC
1 TGGCCAAAAATTGAGGAAAAATTTTTCGGATCAATTTTTGCAAAATTTTAGCCGAAATCATGTAC
* * *
2390 TATTCATCACGAGTTTTGGCTAAAAACGCG-TTCCAGGGCTCAGGCTCAATTTTGCATGATTTTT
66 TA-TCA-CA-G-TTTTTGGCTAAAAACGCGTTTCAAGGCCTC-GGCTCAATTTTGCATGATTTTT
* * * *
2454 GGAGCCCAGAACCCTTGAAATTTCAATATTCATCTAACCAAATCTCAACCACATTGAATTTGAAA
126 GGCGCCTAGAACCCTTGAAA-TTCTATATTCATCTAACCAAATCTCAACCACATTGAATTTAAAA
*
2519 ATTTGATTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGGAATTAATTCCGAAAAAATGGG
190 ATTTGATTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGGAATTAATT-C-AAAAAATGGG
* *
2584 AAAACGATATTAGAAGCGTGAAAAGCTCTTCAATA-TATTTGGTGTTGAATTATATATTTTTTCC
253 AAAACGATATTAGAAGCGTGAAAAGC-CTTCAATACT-TTTGGCGTTGAATTATATA-TTTGTCC
*
2648 -GAGTATAG
315 TAAGTATAG
* * *
2656 TTGCCAAAAATTGAGGAAAAATTTTTCCGATCAATTTTTGCAAAATTTTAGCCGAAATCTTGTAC
1 TGGCCAAAAATTGAGGAAAAATTTTTCGGATCAATTTTTGCAAAATTTTAGCCGAAATCATGTAC
* *
2721 TATCACAGTTTTTTGCTAAAAACGCGTTTCAAGGCCTCGGCTCAATTTTGCATGAATTTTGGCGC
66 TATCACAGTTTTTGGCTAAAAACGCGTTTCAAGGCCTCGGCTCAATTTTGCATGATTTTTGGCGC
* * * * *
2786 CTAGAGCCCTTGAAATTACTATATCCATCTAACCAAATCTCAGCCACATCGAATTCAAAAATTTG
131 CTAGAACCCTTGAAATT-CTATATTCATCTAACCAAATCTCAACCACATTGAATTTAAAAATTTG
* * * * ** *
2851 ATTTTAAGAGCATCTGAATTTTGTTTTGATTTAATTAGAAATTAATTCAAAAAAATGAAAAAATG
195 ATTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGGAATTAATTC-AAAAAATGGGAAAACG
*
2916 ATATTAGAATCGTGAAAAGCCCTTCAAT-CTTTTTGGCGT
259 ATATTAGAAGCGTGAAAAG-CCTTCAATAC-TTTTGGCGT
2955 ACAAATATAT
Statistics
Matches: 540, Mismatches: 64, Indels: 46
0.83 0.10 0.07
Matches are distributed among these distances:
316 1 0.00
317 3 0.01
318 2 0.00
319 8 0.01
320 178 0.33
321 11 0.02
322 1 0.00
324 4 0.01
326 48 0.09
327 139 0.26
328 10 0.02
329 2 0.00
330 34 0.06
331 93 0.17
332 6 0.01
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (323 bp):
TGGCCAAAAATTGAGGAAAAATTTTTCGGATCAATTTTTGCAAAATTTTAGCCGAAATCATGTAC
TATCACAGTTTTTGGCTAAAAACGCGTTTCAAGGCCTCGGCTCAATTTTGCATGATTTTTGGCGC
CTAGAACCCTTGAAATTCTATATTCATCTAACCAAATCTCAACCACATTGAATTTAAAAATTTGA
TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGGAATTAATTCAAAAAATGGGAAAACGAT
ATTAGAAGCGTGAAAAGCCTTCAATACTTTTGGCGTTGAATTATATATTTGTCCTAAGTATAG
Found at i:4924 original size:62 final size:62
Alignment explanation
Indices: 4825--5106 Score: 519
Period size: 62 Copynumber: 4.5 Consensus size: 62
4815 ACTTAACAAG
* *
4825 GCAGACACGATGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
1 GCAGGCACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
*
4887 GCAGGCACGAAGGCACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
1 GCAGGCACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
*
4949 ACAGGCACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
1 GCAGGCACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
*
5011 GCAGGCACGAAGGTACACGAGAAGACAGGGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
1 GCAGGCACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
5073 GCAGGCACGAAGGTACACGAGAAGACAGAGGAAG
1 GCAGGCACGAAGGTACACGAGAAGACAGAGGAAG
5107 ACAGACACGA
Statistics
Matches: 212, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 212 1.00
ACGTcount: A:0.35, C:0.22, G:0.40, T:0.03
Consensus pattern (62 bp):
GCAGGCACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
Found at i:5121 original size:34 final size:34
Alignment explanation
Indices: 5078--5144 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
5068 GGCCAGCAGG
*
5078 CACGAAGGTACACGAGAAGACAGAGGAAGACAGA
1 CACGAAGGTAAACGAGAAGACAGAGGAAGACAGA
5112 CACGAAGGTAAACGAGAAGACAGAGGAAGACAG
1 CACGAAGGTAAACGAGAAGACAGAGGAAGACAG
5145 GAAGACACAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.48, C:0.16, G:0.33, T:0.03
Consensus pattern (34 bp):
CACGAAGGTAAACGAGAAGACAGAGGAAGACAGA
Found at i:5269 original size:2 final size:2
Alignment explanation
Indices: 5264--5288 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5254 ACACACACAG
5264 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
5289 CAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Done.